Refactor phylogenetic such that a reasonable phylogenetic/build-configs/ci works

[j23414]

Context

While adding
https://github.com/nextstrain/pathogen-repo-guide/tree/main/phylogenetic/build-configs/ci
realized phylogenetic was reading directly from ingest/results/ in

WNV/phylogenetic/defaults/config.yaml

Lines 9 to 10 in 9c521cc

	input_metadata: "../ingest/results/metadata_all.tsv"
	input_sequences: "../ingest/results/sequences_all.fasta"

This may need to be refactored to work with our automation setup.

Description

• Add example sequences
• Instead of taking ingest/results/* as input, add a download or copy rule to prepare_sequences.smk
• Add phylogenetic/build-configs/ci check

Examples

Possible solution

(Optional)

[j23414]

Closed since the last task was completed at ec5dd33